Fig. 5

Imputation accuracy on chromosome 19 by density of framework marker panel. A) Accuracy for an optimal set of dense markers on chromosome 19, using 4 individuals with WGS data, imputed into all remaining pedigree members with GBS data. Circles denote individual animals as indicated in the legend; we note that not every individual may be distinguished in these graphs due to overlapping values. Framework marker panels were designed by selecting positions with GBS data that intersect with SNVs of MAF >0.25. Three framework panels were tested: 325 SNVs present in all 16 individuals (Panel A); 811 SNVs present in 8/16 individuals (Panel B); 1,027 SNVs present in 4/16 individuals (Panel C), and 2,737 SNVs that include all sites with high-confidence genotypes in the GBS data (All sites). B) The fraction of dense markers imputed using hard probability thresholds for calling genotypes, as described in Results